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Yorodumi- PDB-6bg7: Crystal structure of G107A mutant of human macrophage migration i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bg7 | ||||||
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Title | Crystal structure of G107A mutant of human macrophage migration inhibitory factor | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE / surface / mutation | ||||||
Function / homology | Function and homology information positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of mature B cell apoptotic process / negative regulation of macrophage chemotaxis / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / carboxylic acid metabolic process / regulation of macrophage activation / negative regulation of protein metabolic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / protein homotrimerization / positive regulation of protein kinase A signaling / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of fibroblast proliferation / cellular senescence / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Pantouris, G. / Lolis, E. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Nanosecond Dynamics Regulate the MIF-Induced Activity of CD74. Authors: Pantouris, G. / Ho, J. / Shah, D. / Syed, M.A. / Leng, L. / Bhandari, V. / Bucala, R. / Batista, V.S. / Loria, J.P. / Lolis, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bg7.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bg7.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/6bg7 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/6bg7 | HTTPS FTP |
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-Related structure data
Related structure data | 5eizC 5uzyC 6bg6C 3djhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 12369.081 Da / Num. of mol.: 3 / Mutation: G107A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 M ammonium sulfate, 3% 2-propanol, 0.1 M Tris-HCl, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 2, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→50 Å / Num. obs: 15576 / % possible obs: 83.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.054 / Rrim(I) all: 0.099 / Χ2: 0.822 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DJH Resolution: 2.54→47.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.156 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.263 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.26 Å2 / Biso mean: 35.66 Å2 / Biso min: 1 Å2
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Refinement step | Cycle: final / Resolution: 2.54→47.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.54→2.606 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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